Gary - You're probably asking the exact wrong guy, because I'm so OCD about stuff like this, I would remedy it just because it would irk me. As I'm talking to a guy that spent upwards of 10 hours on his back steam cleaning the underside of his E12, we may have something in common in this regard.
But I suspect there may be good reasons to fix this apart from aesthetics. That is if the wobble persists at high speed. It sounds like you've diagnosed the wobble while manually rotating the fan, and it's possible that it could correct itself at high speed. But if you've "locked in" the warp of the metal plate it may not. Also, if you've changed your clutch, you can't be sure the wobble isn't there.
One reason to correct is that when you switch to the spin-on mounting, you may find as I did that the fan rides closer to the rad. A wobble, if it's pronounced enough, may be enough for the fan blades to contact the rad fins. At 2500 RPM, the unbalance (if it persists) will cause greater wobble. The forces involved can be large even though the unbalance is rather small.
Absent interference with the rad, I would be concerned about the life of your water pump bearing. What a wobble really does is make the true axis of rotation dynamically deviate from the mechanical axis, and that means a lateral force will be transmitted to the pulley, the flange and then to the pump bearing (in other words, a force in the plane of the fan). In the math for calculating this force, because the fan is at the end of the axis of rotation, it's the farthest from the bearing so that increases the force of the deflection. The mass of the pulley and flange is then recruited into the wobbling system, which also increases the force generated. And the high rotational speed is actually the real driver of the force generation (in the math, rotational speed is squared).
Sustained vibration forces like this over time are bad for bearings, so I would probably do what I could to correct it. That said, now that you'll have a spin-on fan, it will be easier to replace the water pump if you need to!
I don't think that removing the fan clutch would create a wobble in the fan, but I don't have any experience with this.